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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git]
/
src
/
jalview
/
datamodel
/
Alignment.java
diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
cfd6aee
..
73ccdc5
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-2057,7
+2057,7
@@
public class Alignment implements AlignmentI, AutoCloseable
if (cm == null && _aa.sequenceRef != null)
{
cm = _aa.sequenceRef.getContactMatrixFor(_aa);
if (cm == null && _aa.sequenceRef != null)
{
cm = _aa.sequenceRef.getContactMatrixFor(_aa);
- if (cm == null && _aa.sequenceRef.getDatasetSequence()!=null)
+ if (cm == null && _aa.sequenceRef.getDatasetSequence() != null)
{
// TODO fix up this logic and unify with getContactListFor
cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa);
{
// TODO fix up this logic and unify with getContactListFor
cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa);
@@
-2069,6
+2069,11
@@
public class Alignment implements AlignmentI, AutoCloseable
@Override
public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
{
@Override
public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
{
+ if (_aa.annotations == null || column >= _aa.annotations.length
+ || column < 0)
+ {
+ return null;
+ }
ContactListI cl = cmholder.getContactListFor(_aa, column);
if (cl == null && _aa.groupRef != null)
{
ContactListI cl = cmholder.getContactListFor(_aa, column);
if (cl == null && _aa.groupRef != null)
{